just upgraded from 1.5 to 3.0.0.422.
In 1.5 I could see in the Organiszation - 'mailbox backup job overview' and rightlick on job: "Edit -> Add" GUI windows the "left over" (unprotected) mailboxes in my O365 exchange.
In 3.0 I can see my entire organisation with the thousands of old deactive Active Directory accounts (we are not allowed to delete an AD account to prevent unique logins to be reused later for security reasons.).
I am shown all accounts: protected and unprotected and all those deactivated legacy user accounts.

I know I can run a report, but that is circumstantially (difficult, boring, time consuming, annoying, i have to search and find etc. etc.) compared to the GUI in V1.5 just showing me the ones left who should be protected.

I use this method for making sure new users mailbox are backed up, a daily task.

How do I in V3 easily see, just like in V1.5, the active (O365 licensed), unprotected mailboxes that VBO needs to backup?
I want to see it in GUI and not using Powershell, generate a report, match a list, search and find - just a GUI listing unprotected but O365 licensed active mailboxes.

As you may have noticed, version 3 provides more backup options and, for Exchange Online, is now based on users and groups rather than mailboxes (as it was in the 1.5). For easier management of users in backup jobs, we recommended using O365 dynamic groups. This approach allows making sure the new users are protected automatically.

The information on the unprotected users' mailboxes is not available in the UI - as you noticed you can get it with the built-in Mailbox Protection report or by using PowerShell. However, your concerns on the additional manual operations make sense, and we'll take it as a feature request for the future versions.